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Case ReportA Rare, Recurrent, De Novo 14q32.2q32.31 Microdeletionof 1.1 Mb in a 20-Year-Old Female Patient with a MaternalUPD(14)-Like Phenotype and Intellectual Disability

Almira Zada,1,2 Farmaditya E. P. Mundhofir,2 Rolph Pfundt,1 Nico Leijsten,1

Willy Nillesen,1 Sultana M. H. Faradz,2 and Nicole de Leeuw1

1 Department of Human Genetics, Radboud University Medical Center, The Netherlands Division of Human Genetics, P.O. Box 9101,6500 HB Nijmegen, The Netherlands

2 Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, GSG 2nd Floor, Jl. Dr. Sutomo 14,Semarang 50244, Indonesia

Correspondence should be addressed to Almira Zada; [email protected]

Received 27 December 2013; Accepted 19 February 2014; Published 30 March 2014

Academic Editors: C. Lopez Gines and G. Perez de Nanclares

Copyright © 2014 Almira Zada et al. This is an open access article distributed under the Creative Commons Attribution License,which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

We present a 20-year-old female patient from Indonesia with intellectual disability (ID), proportionate short stature, motordelay, feeding problems, microcephaly, facial dysmorphism, and precocious puberty who was previously screened normal forconventional karyotyping, fragile X testing, and subtelomeric MLPA analysis. Subsequent genome wide array analysis wasperformed on DNA from blood and revealed a 1.1Mb deletion in 14q32.2q32.31 (chr14:100,388,343-101,506,214; hg19). Subsequentcarrier testing in the parents by array showed that the deletion had occurred de novo in the patient and that her paternal 14q32allele was deleted. The deleted region encompasses the DLK1/GTL2 imprinted gene cluster which is consistent with the maternalUPD(14)-like phenotype of the patient. This rare, recurrent microdeletion was recently shown not to be mediated by low copyrepeats, but by expanded TGG repeats, flanking the 14q32.2q32.21 deletion boundaries, a novel mechanism of recurrent genomicrearrangement. This is another example how the application of high resolution genome wide testing provides an accurate geneticdiagnosis, thereby improving the care for patients and optimizing the counselling for family.

1. Introduction

Theapplication of high resolution genomewide array analysisprovides an accurate genetic diagnosis in many patientswith ID and/or congenital anomalies caused by genomicimbalances. The use of this technology has led to the dis-covery of several novel microdeletion and microduplicationsyndromes. Although several patients have been reportedwith a terminal 14q32 deletion, patients with an in terstitialmicrodeletion in the 14q32 region seem to be rare. To ourknowledge, only two patients with an interstitial 1.1Mbdeletion in q32.2q32.31 have previously been reported [1, 2].

Human chromosome 14q32.2 is the critical region for uni-parental disomy of chromosome 14 (UPD(14)) phenotypesbecause it carries a cluster of imprinted genes, including thepaternally expressed genes (PEGs) such as DLK1&RTL1 and

the maternally expressed genes (MEGs) such as GTL2 (alsoknown asMEG3),RTL1as (RTL1 antisense), andMEG8.Dele-tion of the paternal allele in this region causes a UPD(14)mat-like phenotype [3]. Uniparental disomy (UPD) occurs whenthe two copies of a chromosome pair are inherited fromonly one parent [4]. Maternal UPD of chromosome 14(UPD(14)mat) is characterized by pre- and postnatal growthretardation, hypotonia, feeding problems, motor delay, shortstature, early onset of puberty, and minor dysmorphic fea-tures of the face, hands, and feet [5]. Seven out of elevenUPD(14)mat-like cases without UPD have been reported tocarry a deletion in the 14q32.2 region [2, 3, 6–9].

Here we report an additional female patient with a1.1Mb deletion of chromosome 14 in the q32.2q32.31 regionidentified by high resolution genome wide SNP array analy-sis.

Hindawi Publishing CorporationCase Reports in GeneticsVolume 2014, Article ID 530134, 5 pageshttp://dx.doi.org/10.1155/2014/530134

http://dx.doi.org/10.1155/2014/530134

2 Case Reports in Genetics

(a) (b) (c)

(d) (e)

Figure 1: Photograph of Indonesian patient with a 14q32.2 microdeletion. Our 20-year-old patient showed extremely short and thin stature,flat face, flat philtrum, thin lips, tapering fingers, clinodactyly of the fifth finger on the right hand, and clubbing feet toes.

2. Case Report

A 20-year-old female Indonesian Javanese patient presentedwith extremely thin and short stature, microcephaly, motordelay, hypotonia, mild intellectual disability, flat face, flatphiltrum, thin lips, tapering fingers, clinodactyly of her fifthfinger on the right hand, clubbing feet toes, feeding problems,and precocious puberty (Figure 1). She was born at 32 weeksof pregnancy with a low birth weight of 1,800 g (p5–10) asthe second child of healthy, unrelated parents. At the timeof her birth, her mother was 24 years of age, and her fatherwas 33 years of age.There was no family history of intellectualdisability. Postnatally, she was found to have feeding problem,motor delay, hypotonia, and precocious puberty. She wasable to walk at three years of age and able to speak at twoyears of age. When she was examined at 20 years of age,her body height was 130 cm (𝑃 < 3), her weight was 18 kg(𝑃 < 3), and her arm spanwas 125 cm.Her ratio height to armspan was 0.96 cm, thus showing proportionate short stature.She has microcephaly with an occipital frontal circumference(OFC) of 50 cm (𝑃 < 3). Previously, genetic tests were done,including conventional karyotyping, subtelomeric MLPA,and fragile X testing, all of which showed normal results [10].Informed consent for publishing results and photos has beenobtained from the patient’s parents.

We performed genome wide array analysis on DNAfrom blood using the Affymetrix CytoScan HD Array plat-form (Affymetrix, Inc., Santa Clara, CA, USA) followingthe manufacturer’s protocols, which showed a 1.1Mb dele-tion in 14q32.2q32.31 (chr14:100,388,343-101,506,214; hg19) asdepicted in Figure 2(a). Subsequent carrier testing with thesame array platform in the parents revealed that the deletionhad occurred de novo in the patient (Figure 2(b)) and thather paternal 14q32 allele was deleted. The possible presenceof either a balanced chromosomal rearrangement and/ormosaic imbalance in the father was subsequently studiedby fluorescence in situ hybridization (FISH) analysis usinga FISH probe (RP11-123M6; BlueGnome Ltd., Cambridge,UK) specific for the 14q32.2q32.31 region. These FISH resultsshowed that the father did not carry a balanced rearrange-ment and/or mosaic imbalance (Figure 3).

3. Discussion

Here we report an additional patient with a rare, recurrent,de novo 14q32.2q32.31 microdeletion of 1.1Mb. Two other(female) patients have been reported in the literature with asimilar 1.1Mb microdeletion in 14q32.2q32.31 [1, 2]. Compa-rable to our patient, it concerned a de novo loss of paternal

Case Reports in Genetics 3

v

(a)

Patient

Mother

Father

(b)

Figure 2: (a) Array plots of chromosome 14, visualized using the Affymetrix Chromosome Analysis Suite (ChAS) Software. A 1.1Mb lossin 14q32.2q32.31 was detected in Patient 1 (arr[hg19] 14q32.2q32.31(100,388,343-101,506,214)x1 dn) as indicated by the red rectangle. (b) Trioanalysis confirms that the deletion has occurred de novo in the patient.

Patient

Del(14)

Del(14)

(a)

(14)

(14)

Father

(b)

Figure 3: FISH study in the patient and her father. In each of them, 30metaphases from cultured peripheral blood lymphocytes were analysed.(a) Patientmetaphase showing one normal chromosome 14 [RP11-123M6 (green)/14 qter 9 (red)] and the del(14)(q32.2q32.31) with only 14 qtersignal (red). (b) Metaphase from the father with a normal FISH pattern, indicating two normal chromosomes 14.

14q32 allele in both patients, who exhibited clinical featurescompatible with UPD-(14)-mat (genomic coordinates andclinical features in hg 19 are shown in Table 1).

This deleted region comprises a snoRNA, part of amicroRNA cluster, and 15 protein-coding genes, containinga cluster of imprinted genes including paternally expressedgenes DLK1&RTL1 and maternally expressed genes GTL2(also known as MEG3), RTL1as, and MEG8. The deletedpaternal 14q32 allele causes a maternal UPD(14)-like phe-notype [3]. The other 10 genes are not imprinted (EVL,DEGS2, YY1, SLC25A29, c14orf68, WARS, WDR25, BEGAIN,c14orf70, and the 3’end of EML1).

Other than pre- and postnatal growth retardation, preco-cious puberty, and feeding problems, which are compatiblewith UPD(14)mat phenotypes, the patient reported here alsomanifested intellectual disability (ID) which is not or rarelyobserved in patients with UPD(14)mat. Considering that the1.1Mb 14q32 deletion also encompasses many nonimprinted

genes, it is likely that the ID in this patient is caused byhaploinsufficiency of one or more dosage-sensitive genes.For example, the BEGAIN (brain-enriched guanylate kinase-associated protein) gene represents a good candidate basedon its localization in the neuronal synapse [11]. The recentlyreported YY1 gene is considered to be an ID disease genebased on the exome sequencing in a patient with unex-plained ID in whom a missense mutation c.1138G>T withprotein level change p.Asp380Tyr was found [12]. This geneimplicates chromatin remodelling as its main function byencoding the ubiquitously expressed transcription factoryin-yang 1 and directing histone acetylases and histoneacetyltransferases. Experiments with Yy1 knockdown miceresulted in growth retardation, neurulation defects, and brainabnormalities [13].

Most recurrent genomic rearrangements are due to non-allelic homologous recombination (NAHR) between mis-aligned low copy repeats resulting in a microdeletion or

4 Case Reports in Genetics

Table 1: Genomic coordinates and clinical features of all cases.

Buiting et al., 2008 [2] Bena et al., 2010 [1] Present caseDeletion positions (Mb) inchromosome 14 (hg 19) 100.396–101.502 100.400–101.500 100.388–101.506

Sex Female Female Female

Age (years) 14 14

4 20

Pre- and postnatal growthretardation + + +

Hypotonia + + +Feeding problems + + +Precocious puberty + ? +Intellectual disability + + +

Dysmorphism −

High forehead, small chin,posteriorly rotated ears, and flatfeet

Flat face, flat philtrum, thin lips,tapering fingers, clinodactyly of thefifth finger on the right hand, andclubbing feet toes

Others − Hypermetropia −

+: present; −: not present; ?: undetermined yet.

a microduplication [14]. However, a recent paper by Benaet al. [1] reported the observations regarding the mecha-nism underlying the recurrent 14q32.2 deletion describedhere. They found that large (TGG)n tandem repeat tractsof about 500 bp are at both boundaries of the dele-tion (chr14:100,394,091-100,394,594 and chr14:101,504,592-101,505,016; hg19). The TGG repeats are the longest typeof triplets motif and highly capable of forming G4 DNA.Some theories might explain how these triplet repeatscan cause genomic rearrangement. First, expanded tripletrepeats would provide an aggravated substrate for genomicrearrangement through the NAHR mechanism [15, 16].Second, expanded triplet repeats have the tendency toform intramolecular secondary structures termed guaninequadruplexes or G4 DNA which could promote doublestrand chromosome breaks [17]. Therefore, it is suggestedthat this recurrent 14q32.2 microdeletion is mediated byexpanded TGG repeats, a novel mechanism of recurrentgenomic rearrangement that is shown not to be mediated bylow copy repeats.

In conclusion, we were able to detect a rarely identified14q32.2 microdeletion by using high resolution genome widearray analysis in a patient whose genotype and phenotypeare in agreement with those of two previously reportedpatients in the literature. This case report demonstrates thevalue of applying high resolution genome wide testing foraccurate genetic diagnosis that can help to improve the carefor patients and to optimize the counselling for family.

Conflict of Interests

The authors declare that there is no conflict of interestsregarding the publication of this paper.

Acknowledgments

This research study was partly funded by the Excellent Schol-arship Program of the Bureau of Planning and InternationalCooperation, Ministry of National Education, Governmentof Indonesia, in collaboration with the Radboud UniversityMedical Centre (Radboud UMC) in Nijmegen, The Nether-lands. The authors thank the family for their cooperationand permission to publish this paper. They also thank thelaboratory staff of Department of Human Genetics, RadboudUMC, Nijmegen, The Netherlands, and CEBIOR, Faculty ofMedicine, Diponegoro University, Semarang, Indonesia.

References

[1] F. Bena, S. Gimelli, E. Migliavacca et al., “A recurrent 14q32.2microdeletion mediated by expanded TGG repeats,” HumanMolecular Genetics, vol. 19, no. 10, pp. 1967–1973, 2010.

[2] K. Buiting, D. Kanber, J. I. Martın-Subero et al., “Clinicalfeatures of maternal uniparental disomy 14 in patients with anepimutation and a deletion of the imprinted DLK1/GTL2 genecluster,” Human Mutation, vol. 29, no. 9, pp. 1141–1146, 2008.

[3] M. Kagami, Y. Sekita, G. Nishimura et al., “Deletions andepimutations affecting the human 14q32.2 imprinted region inindividuals with paternal and maternal upd(14)-like pheno-types,” Nature Genetics, vol. 40, no. 2, pp. 237–242, 2008.

[4] E. Engel, “A new genetic concept: uniparental disomy andits potential effect, isodisomy,” American Journal of MedicalGenetics, vol. 6, no. 2, pp. 137–143, 1980.

[5] V. R. Sutton and L. G. Shaffer, “Search for imprinted regionson Chromosome 14: comparison of maternal and paternal UPDcases with cases of chromosome 14 deletions,”American Journalof Medical Genetics, vol. 93, pp. 381–387, 2000.

[6] D. Mitter, K. Buiting, F. Von Eggeling et al., “Is there a higherincidence of maternal uniparental disomy 14 [upd(14)mat]?Detection of 10 new patients by methylation-specific PCR,”

Case Reports in Genetics 5

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[7] K. Hosoki, T. Ogata, M. Kagami, T. Tanaka, and S. Saitoh,“Epimutation (hypomethylation) affecting the chromosome14q32.2 imprinted region in a girl with upd(14)mat-like pheno-type,” European Journal of Human Genetics, vol. 16, no. 8, pp.1019–1023, 2008.

[8] A. Schneider, B. Benzacken, A. Guichet et al., “Molecularcytogenetic characterization of terminal 14q32 deletions in twochildren with an abnormal phenotype and corpus callosumhypoplasia,” European Journal of Human Genetics, vol. 16, no.6, pp. 680–687, 2008.

[9] U. Zechner, N. Kohlschmidt, G. Rittner et al., “Epimutation athuman chromosome 14q32.2 in a boy with a upd(14)mat-likeclinical phenotype,” Clinical Genetics, vol. 75, no. 3, pp. 251–258,2009.

[10] F. E. Mundhofir, T. I. Winarni, B. W. van Bon et al., “Acytogenetic study in a large population of intellectually disabledIndonesians,” Genetic Test Molecular Biomarkers, vol. 16, pp.412–417, 2012.

[11] I. Yao, J. Iida, W. Nishimura, and Y. Hata, “Synaptic and nuclearlocalization of brain-enriched guanylate kinase-associated pro-tein,” Journal of Neuroscience, vol. 22, no. 13, pp. 5354–5364,2002.

[12] L. E. L. M. Vissers, J. De Ligt, C. Gilissen et al., “A de novoparadigm for mental retardation,” Nature Genetics, vol. 42, no.12, pp. 1109–1112, 2010.

[13] Y. He and P. Casaccia-Bonnefil, “The Yin and Yang of YY1 in thenervous system,” Journal of Neurochemistry, vol. 106, no. 4, pp.1493–1502, 2008.

[14] P. J. Hastings, J. R. Lupski, S. M. Rosenberg, and G. Ira,“Mechanisms of change in gene copy number,” Nature ReviewsGenetics, vol. 10, no. 8, pp. 551–564, 2009.

[15] J. Rubnitz and S. Subramani, “Theminimum amount of homol-ogy required for homologous recombination in mammaliancells,” Molecular and Cellular Biology, vol. 4, no. 11, pp. 2253–2258, 1984.

[16] A. S. Waldman and R. M. Liskay, “Dependence of intrachro-mosomal recombination in mammalian cells on uninterruptedhomology,” Molecular and Cellular Biology, vol. 8, no. 12, pp.5350–5357, 1988.

[17] K. Usdin, “NGG-triplet repeats form similar intrastrand struc-tures: implications for the triplet expansion diseases,” NucleicAcids Research, vol. 26, no. 17, pp. 4078–4085, 1998.

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